feat: add parameter parser class

src/parameter_parser.py

+"""Module containing functionalities to store run parameters.
+
+Class:
+    ParamParse: Take as input a file containing the parameters
+    and stores them in its attributes.
+"""
+import logging
+from pathlib import Path
+
+LOG = logging.getLogger(__name__)
+
+
+class ParamParse:
+    """Class holding the parameters of the run.
+
+    Args:
+        param_file: Path to file with parameter values.
+
+    Attributes:
+        param_file: File with parameter values.
+        transcripts_file: File with transcript abundances.
+        genome_ref_file: Reference genome file.
+        annotations_file: Transcripts annotations.
+        output_path: Output folder.
+        n_reads: Number of reads to be simulated.
+        n_cells: Number of cells to be simulated.
+        rna_avg_length: average RNA fragment length.
+        rna_sd_length: RNA fragment length standard deviation.
+        read_length: Read length.
+        intron_rate: Constant probability of retaining an intron.
+        add_poly_a: Boolean option to add a poly A tail.
+        poly_a_func: Function to add a poly_a tail.
+        primer_seq: Sequence of the primer.
+        priming_func: Function that evaluates internal priming.
+    """
+
+    def __init__(self, param_file: Path) -> None:
+        """Class constructor."""
+        self.param_file: Path = Path(param_file)
+        with open(param_file) as f:
+            LOG.info("Loading parameters...")
+            for line in f:
+                s = line.split(':')
+                if s[0] == 'Csv transcripts file':
+                    self.transcripts_file: Path = Path(s[1].strip())
+                elif s[0] == 'Reference genome file':
+                    self.genome_ref_file: Path = Path(s[1].strip())
+                elif s[0] == 'Transcripts annotation file':
+                    self.annotations_file: Path = Path(s[1].strip())
+                elif s[0] == 'Output folder':
+                    self.output_path: Path = Path(s[1].strip())
+                elif s[0] == 'Number of reads':
+                    self.n_reads: int = int(s[1].strip())
+                elif s[0] == 'Number of cells':
+                    self.n_cells: int = int(s[1].strip())
+                elif s[0] == 'Average RNA fragments length':
+                    self.rna_avg: float = float(s[1].strip())
+                elif s[0] == 'RNA fragment length standard deviation':
+                    self.rna_sd_length: float = float(s[1].strip())
+                elif s[0] == 'Reads length':
+                    self.read_length: int = int(s[1].strip())
+                elif s[0] == 'Intron retaining probability':
+                    self.intron_rate: float = float(s[1].strip())
+                elif s[0] == 'Add poly A tail':
+                    self.add_poly_a: bool = bool(s[1].strip())
+                elif s[0] == 'Function to add poly A tail':
+                    self.poly_a_func: str = str(s[1].strip())
+                elif s[0] == 'Primer sequence':
+                    self.primer_seq: str = str(s[1].strip())
+                elif s[0] == 'Function to evaluate internal priming':
+                    self.priming_func: str = str(s[1].strip())
+        LOG.info("Parameters loaded.")

tests/resources/Param_test.txt

+Csv transcripts file: ./transcripts.csv
+
+Reference genome file: ./home/ref.ref
+
+Transcripts annotation file: ./home/annotations.ann
+
+Output folder: ./home/output
+
+Number of reads: 10023
+
+Number of cells: 34
+
+Average RNA fragments length: 150
+
+RNA fragment length standard deviation: 10
+
+Reads length: 100
+
+Intron retaining probability: 0.2
+
+Add poly A tail: TRUE
+
+Function to add poly A tail: generate_poly_a
+
+Primer sequence: ACCTGATCGTACG
+
+Function to evaluate internal priming: internal_priming
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tests/test_parser.py

+"""Tests the parameter parser class."""
+
+import pytest
+from pathlib import Path
+from src import parameter_parser as pp
+from src import poly_a
+
+def test_parser():
+    """Tests the attributes of the class."""
+    par=pp.ParamParse('./tests/resources/Param_test.txt')
+    assert par.param_file == Path('./tests/resources/Param_test.txt')
+    assert par.transcripts_file == Path('./transcripts.csv')
+    assert par.genome_ref_file == Path('./home/ref.ref')
+    assert par.annotations_file == Path('./home/annotations.ann')
+    assert par.output_path == Path('./home/output')
+    assert par.n_reads == 10023
+    assert par.n_cells == 34
+    assert par.rna_avg == 150
+    assert par.rna_sd_length == 10
+    assert par.read_length == 100
+    assert par.intron_rate == 0.2
+    assert par.add_poly_a == bool('TRUE')
+    assert par.poly_a_func == 'generate_poly_a'
+    assert par.primer_seq == 'ACCTGATCGTACG'
+    assert par.priming_func == 'internal_priming'
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